Database errors after install

Help
1

Basically I’ve run the install script and I get errors reading or writing history that look like this:

Error: error returned from database: (code: 5386) disk I/O error

Caused by:
(code: 5386) disk I/O error

Location:
crates/atuin/src/command/client/history.rs:564:18

I’ve tried wiping the ~/.local/share/atuin and ~/.config/atuin and ~/.atuin folders multiple times, I’ve tried zsh instead of bash. I’ve also coincidently completely replaced the hard drive it’s using too. This is on a standard user account. I’ve installed it for root user and it works perfectly.

2

Hey!

Are you able to share the output of atuin doctor please?

3

For the account it fails on:

~$ atuin doctor
Error: error returned from database: (code: 5386) disk I/O error

Caused by:
(code: 5386) disk I/O error

Location:
crates/atuin/src/command/client.rs:126:18

And for the one that works:

$atuin doctor
Atuin Doctor
Checking for diagnostics

Please include the output below with any bug reports or issues

{
“atuin”: {
“version”: “18.3.0”,
“sync”: null,
“sqlite_version”: “3.44.0”
},
“shell”: {
“name”: “bash”,
“default”: “bash”,
“plugins”: [
“atuin”,
“bash-preexec”
],
“preexec”: “bash-preexec”
},
“system”: {
“os”: “Debian GNU/Linux”,
“arch”: “x86_64”,
“version”: “12”,
“disks”: [
{
“name”: “/dev/nvme0n1p2”,
“filesystem”: “ext4”
},
{
“name”: “/dev/nvme0n1p1”,
“filesystem”: “vfat”
},
{
“name”: “mergerfs”,
“filesystem”: “fuse.mergerfs”
},
{
“name”: “/dev/sdj”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdp”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdi”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdh”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdd”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdc”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sde”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdf”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdk”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdo”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdl”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdg”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdb”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sda”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdn”,
“filesystem”: “ext4”
},
{
“name”: “overlay”,
“filesystem”: “overlay”
},
{
“name”: “/dev/sdm”,
“filesystem”: “ext4”
},
{
“name”: “/dev/sdq”,
“filesystem”: “ext4”
}
]
}
}

4

Can you tell me as much as possible about the disk and filesystem for the one that fails?

5

It’s on a brand new 12 tb ext4 formatted drive (it failed similarly on a smaller drive formatted the same way) that is accessed as part of a mergerfs pool. The working account home folder is not being access via mergerfs.

The fstab entry for the pool looks like:

# mergerfs pool
/mnt/disk* /srv/storage fuse.mergerfs direct_io,defaults,allow_other,minfreespace=50G,fsname=mergerfs,cache.files=off,dropcacheonclose=true,category.create=mfs 0 0

6

Are you able to try without mergerfs? From a brief look at their repo, there can be perf and other issues with sqlite

7

Mergerfs does indeed seem to be the culprit, moving the home folder else where allows it to work.

8

Ok, so with a bit of experimenting I’ve manged to get it to work. For anyone in the future that has this problem cache.files=off was causing my issue, setting it to partial instead of off makes atuin work correctly. I guess this is an sqlite3/mmap issue.

thanks for the help ellie

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